Recent discovery of type II fatty acid synthase in the malarial parasite Plasmodium falciparum responsible for the most debilitating form of the disease in humans makes it ideal as a target for the development of novel antimalarials. Also, the identification of the enoyl-acyl carrier protein reductase from P. falciparum and the demonstration of its inhibition by triclosan [5-chloro-2-(2,4-dichlorophenoxy)phenol], a potent antibacterial compound, provide strong support for the above. In the studies reported here, a model of the enzyme in complex with triclosan and the cofactor NAD has been built by homology modeling with a view to understand its binding properties and to explore the potential of triclosan as a lead compound in designing effective antimalarial drugs. The model indeed provided the structural rationale for its interaction with ligands and the cofactor and revealed unique characteristics of its binding site which could be exploited for improving the specificity of the inhibitors.